modules/fcs_fcsgx

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

assemblygenomicsquality controlcontaminationNCBI

https://github.com/nf-core/modules/[...]/modules/nf-core/fcs/fcsgx

Description

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘6973’ ]

`assembly:file`

assembly fasta file

`gxdb:file`

The NCBI GenBank database to search against.

Output

name:type

description

pattern

`fcs_gx_report`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘9606’ ]

`out/*.fcs_gx_report.txt:file`

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

`taxonomy_report`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘9606’ ]

`out/*.taxonomy.rpt:file`

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

fcs

"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."

ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools github.com/ncbi/fcs/wiki/FCS-GX https://github.com/ncbi/fcs